A various types of nucleic acid-acting proteins are involved in the control of structural transition of nucleic acid hybrids within an organism.
The nucleocapsid (NC) protein in retrovirus transfers DNA chain from one hybrid to more stable hybrid and plays some roles in viral infection ((a) Z. Tsuchihashi and P. O. Brown, J. Virol. 68, 5863(1994); (b) M, Lapadat-Tapolsky, C. Pornelle, C. Borie and J-L. Darlix, Nucleic Acids Res. 23, 2434 (1995)). NC protein has an activity to stimulate destruction and reassembly of base pairs, and acts as a nucleic acid chaperon to help appropriate hybridization of nucleic acids. ((a) W. Wu, L. E. Henderson, T. D. Copeland, R. J. Gorelick, W. J. Bosche, A. Rein and J. G. Levin, J. Virol. 70, 7132 (1996); (b) X. Ji, G. J. Klarmann and B. D. Preston, Biochemistry 35, 132 (1996); (c) V. Tanchou, C. Gabus, V. Rogemond and J-L. Darlix, J. Mol. Biol. 252,563 (1995)).
RecA protein has a multivalent binding site to DNA and forms an intermediate complex with double stranded DNA (dsDNA) and single stranded DNA (ssDNA). ((a) J. W. Roberts, C. W. Roberts, N. L. Craig and E. M. Phizicky, Cold Spring Harbor Symp. Quant. Biol. 43,917 (1979); (b) T. Shibata, C. DasGupta, R. P. Cunningham and C. M. Radding, Proc. Natl. Acad. Sci. USA 76, 1638 (1979); (c) K. Mcentee, G. M. Weinstock and I. R. Lehman, Proc. Natl. Acad. Sci. USA 76, 2615 (1979); (d) E. Cassuto, S. C. West, J. Mursalim, S. Conlon and P. Howard-Flanders, Proc. Natl. Acad. Sci. USA 77 and 3962 (1980)).
Since the sequence specificity and assembly property of a nucleic acid molecule are fully elucidated, they can be used for a molecular construction having a desirable structure at a molecular level. A various types of molecules such as a DNA molecule machine ((a) B. Yurke, A. J. Turberfield, A. P. Mills Jr., F. C. Simmel and J. L. Neumann, Nature 406, 605 (2000); (b) H. Yan, X. Zhang, Z. Shen and N. C. Seeman, Nature 415 and 62 (2002)), a nano assembly ((a) B. Liu, N. B. Leontis and N. C. Seeman, Nanobiology 3, 177 (1994);
(b) E. Winfree, F. Liu, L. A. Wenzler and N. C. Seeman, Nature 394, 539 (1998)), and a molecule computer ((a) L. M. Adleman, Science 266, 1021 (1994) ; (b) K. Sakamoto, H. Gouzu, K. Komiya, D. Kiga, S. Yokoyama, T. Yokomori, and M. Hagiya, Science 288, 1223 (2000)) are proposed. Therefore, an artificial substance that can manipulate structural transition of a nucleic acid molecule will be a useful tool not only in the biotechnology field but in the nanotechnology field.
The inventors already have reported interaction between cationic comb-type copolymer (Cationic comb-type copolymers: CCCs) comprising cationic poly(L-lysine) (PLL) backbone and water-soluble side chain of dextran and DNA (A. Maruyama, M. Katoh, T. Ishihara and T. Akaike, Bioconjugate Chem. 8, 3 (1997); A. Maruyama, H. Watanabe, A. Ferdous, M. Katoh, T. Ishihara and T. Akaike, Bioconjugate Chem. 9,292 (1998)). A comb-type copolymer with a higher degree of grafting accelerates DNA hybridization (H. Torigoe, A. Ferdous, H. Watanabe, T. Akaike and A. Maruyama, J. Biol. Chem. 274, 6161 (1999); A. Ferdous, T. Akaike and A. Maruyama, Bioconjugate Chem. 11, 520 (2000)), and stabilizes the double strand and ternary strand of DNA. Furthermore, it was proved that CCCs stimulate the DNA strand exchange reaction between dsDNA and ssDNA homologous thereto, and accelerates the rate more than spermine and N,N,N-trimethyl hexadecyl ammonium bromide (cetyl trimethyl ammonium bromide: CTAB) (50,000 fold at 37□) (W. J. Kim, T. Ishihara, T. Akaike and A. Maruyama, Chem. Eur. J. 7, 176 (2001)). The copolymer is shown to have nucleic acid chaperon activity and useful in nucleic acid analysis.
A nucleic acid acting protein shares one or more cluster in common comprising basic amino acids, i.e., lysine and arginine. However, the composition of the basic amino acid in these clusters is irregular, and significantly differs among proteins. For example, histon protein contains quite a lot of lysine and arginine residues, while protamin contains little lysine residue (H. Busch, in: Histones and Other Nuclear Proteins, p. 28, Academic Press., New York (1965)). These facts suggest that lysine and arginine may interact with the nucleic acid in a different mechanism. As a basic functional group, lysine has a primary amino group while arginine has a guanidino group.
In physiological pH, the primary amino group and the guanidino group are positively charged. It is reported that in physiological pH, the interaction of the peptide having high content of lysine or arginine with DNA is mainly ionic action, while the interaction of peptide having high content of arginine with DNA or RNA involves hydrogen bond that is stronger than ionic action (F. A. Cotton, V. W. Day, E. E. Hazen Jr. and S. Larsen, J. Am. Chem. Soc. 95, 4834 (1973); G. Lancelot, R. Mayer and C. Helene, Biochem. Biophys. Acta 564, 181 (1979); K. M. Weeks, C. Ampe, S. C. Schultz, T. A. Steitz and D. M. Crothers, Science 249, 1281 (1990)).
Patent document 1: Japanese published unexamined application 2001-78769
Non patent document 1: A. Ferdous, T. Akaike and A. Maruyama, Bioconjugate Chem. 11, 520 (2000)
Non patent document 2: W. J. Kim, T. Ishihara, T. Akaike and A. Maruyama, Chem. Eur. J. 7,176 (2001).